AutoML Template

A template that provides all the tools to ensure the same project setup across all AutoML packages.

You can follow githubs docs for copying the template then follow the commands below to generate the template.

1. On the repo automl_template hit Use this template.
2. Select yourself, the owner of the new repository.
3. Give your repository a name.
4. Make it public/private. If making it private, you'll have automated workflow limits. By default these are disabled but you can navigate to .github/workflows and uncomment everything under on: to enable them.
5. Select Include all branches if you want published docs. May as well even if you don'tn need docs yet!
6. Click Create repository from template

Once you've done those steps, you'll want to download your repo, generate the template and push up your generated template to github.

git clone git@github.com:user/myrepo.git

# Move into the cloned repo
cd myrepo

# Generate the repo , optionally with a predefined config
python generate.py # student publication package

# ... You'll be asked things about your repo, fill them in and confirm

# Add the new repo contents
git add .

# Add a commit with whatever message you like
git commit -m "*mario voice* Wahoooo"
git push

# ... and you're good to go!

Some next steps to do would be to create a virtual environment and use that and then install your repo install your repo with the [dev] requirements that were generated for you. You can find these in setup.py if you're curious!

# Create a virtual env with pythons built in virtualenv
python -m venv myenv
source ./myenv/bin/activate

# ... or using conda
conda create -n myenv python=3.8
conda activate myenv

# Install the repo
make install-dev

# ... or manually
pip install -e ".[dev]"

# If doing manually and you activated the `pre-commit` feature, you'll need to run this too
pre-commit install

You can check out the Makefile where we put some useful commands for your new repo!

make help

Lastly, you can configure your editor to use all these nice new tools :)

Use cases

We support 3 main use cases, which you kind find their features in the table overview:

• student - Includes some checkers with support for testing.
• publication - A repo for a publication, same as student but with some extras included: doc building, formatters, a citation file and a license.
• package - A repo that's planned to have multiple contributors and published to PyPi. Same as publication but with pre-commit to help with code and some utility to help with publishing.

We set some sensible defaults but you'll still be asked about some extra features you can optionally include if you like. You can get a table overview of what's included in or view each individual tool here.

Parameters

You'll be asked about these any time you run generate.py with a brief description.

• name - The name of your github repo when you created the template
• package-name - The name of your package when doing import my_package_name
• author - Your name (and collaborators names)
• organization - The name of your organization. This is your github name www.github.com/<organization>/my_repo_name
• email (optional) - An email address you would like associated with your repo
• description (optional) - A description of your repo
• url (optional) - A url you would like associated with your repo

You can leave any (optional) things blank if not relevant.

Config Table

feature	student	publication	package	empty
testing	✔️	✔️	✔️	❔
flake8	✔️	✔️	✔️	❔
pydocstyle	✔️	✔️	✔️	❔
docs	❌	✔️	✔️	❔
black	❌	✔️	✔️	❔
isort	❌	✔️	✔️	❔
citations	❌	✔️	✔️	❔
license	❌	✔️	✔️	❔
packaging	❌	❌	✔️	❔
pre-commit	❌	❌	✔️	❔
mypy	❔	❔	❔	❔

Features

testing

For testing, we include pytest and also provide a workflow file pytest.yml. The tests can be run locally with pytest or make test while every push will also activate the workflow so you get automated tests on github.

• configuration - pyproject.toml
• run - make test or pytest
• workflow - pytest.yml

flake8

This includes a code checking tool flake8 which checks for common programmer errors and that your code complies with pep8 standards.

• configuration .flake8
• run - make check or flake8 <path>

pydocstyle

This includes pydocstyle to your code to make sure you include some documentation so that anyone reading your code will have a much easier time.

• configuration - pyproject.toml.
• run - make check or pydocstyle <path>

docs

This includes tooling around generating sphinx documentation and provides a nice default theme from automl_sphinx_theme.

This feature will enable github pages and automatically generate your docs which you can view at https://organization.github.io/myreponame/main/. An example of how that looks is here. This also includes a place to put examples which will be run and produce the output into your docs. This is done automatically with a workflow docs.yml. You'll want to add this to your repos home page on the right for easy access ;)

• configuration - docs/conf.py
• run - make docs or make examples inside docs

Your logo and favicon are shown if the files docs/images/logo.png or docs/images/favicon.ico can be found, respectively.

black

This feature will include a formatter called black which automatically formats your code to a stricter version of pep8 standards. This is useful for repos which will have multiple contributors so reviews can focus on the code changes and not stylistic changes.

• configuration - pyproject.toml
• run - make format or black <path>

isort

This feature will include the isort formatter which automatically sorts your imports. For the same reasons as black, this means imports are done in a uniform manner for all contributors.

• configuration - pyproject.toml
• run - make format or isort <path>

citations

This includes a CITATION.cff which allows users to automatically grab a citation from your github repos homepage. It also includes a citation_cff.yml workflow to automatically validate it anytime you update it. You can find more here and more detailed information here.

• workflows - citations_cff.yml

license

If you plan to have others use your code beyond trying things out, you'll want to include a license. By default we only include the Apache2.0 license but you can change this if you require.

pre-commit

This feature enables pre-commit, a tool that integrates with git so that every time you try to commit with git commit or in your editor, such as vscode. This will automatically run any of the checkers you have installed so that it will prompt you to fix errors before you push the code up to the repository.

• configuration - pre-commit-config.yml
• run - make pre-commit or pre-commit run --all-files
• workflows - pre-commit.yml

mypy

The feature we opted to always be optional is mypy. This is a static type checker that works with python's typing module. This can include help catch quite a few errors before any code is even run, similar to how C or Java code won't compile if there's type errors, but allows for gradual typing, allowing you to "type" the parts of the code that matter to you.

If you're not familiar with pythons typing or typing in general, we recommend you keep this feature off

• configuration - pyproject.toml
• run - make check or mypy <path>

Workflows

Workflows are what github uses to automatically run certain things anytime there's a change in the repository. You probably don't need to mess with these files too much but you can find them in the .github/workflows folder. Github's documentation for this is here

By default these are disabled but you can navigate to .github/workflows and uncomment everything under on: to enable them.

citations_cff.yml

This workflow activates whenever you change your CITATION.cff file and validates it.

• path - .github/workflows/citatin_cff.yml

pre-commit.yml

This workflow will run all the checkers and formatters against your code and fail if they don't pass.

• path - .github/workflows/pre-commit.yml

pytest.yml

This workflow will run any tests you have against your code and fail if any of the tests fail

• path .github/workflows/pytest.yml

docs.yml

This workflow will build your documentation and fail if it can't build the docs. If the changes were to the main branch, it will push the new documentation to github pages so it can be viewed publicly

• path - .github/workflows/docs.yml

Configuring your editor

vscode

Just search for the "python" plugin and install it. Your editor should then pick up on all the configuration!

Pycharm

Help wanted, please raise an issue with how to do this :)

Other

If you use other editors and know how to configure them for these tools, raise an issue here and let us know!